Variant report

Variant	rs259695
Chromosome Location	chr6:37884218-37884219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10456096	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10456097	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1074234	0.89[AFR][1000 genomes]
rs10807188	0.84[EUR][1000 genomes]
rs1187422	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187423	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190570	0.82[AFR][1000 genomes]
rs12192182	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12198907	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12200258	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206818	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211248	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211981	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213835	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210701	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13214465	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13220131	0.82[EUR][1000 genomes]
rs16890277	0.81[ASN][1000 genomes]
rs171831	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1812599	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132597	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2395686	0.84[EUR][1000 genomes]
rs259673	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259679	0.98[AFR][1000 genomes]
rs259684	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259686	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259689	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259690	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259691	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259713	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259715	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259716	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2645107	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645113	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645116	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645117	0.83[AFR][1000 genomes]
rs2645120	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2645124	0.85[AFR][1000 genomes]
rs2645127	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2645128	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842500	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842517	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842527	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2842529	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34871463	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35806631	0.82[AFR][1000 genomes]
rs35823566	0.84[ASN][1000 genomes]
rs56098839	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458027	0.85[EUR][1000 genomes]
rs6458028	0.84[EUR][1000 genomes]
rs7755089	0.83[EUR][1000 genomes]
rs9296232	0.84[EUR][1000 genomes]
rs9394460	0.84[EUR][1000 genomes]
rs9647619	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966705	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv970036	chr6:37876765-37894762	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37850600-37890400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:37851000-37884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:37857600-37886000	Weak transcription	Esophagus	oesophagus
4	chr6:37857600-37895400	Weak transcription	Pancreas	Pancrea
5	chr6:37866000-37885600	Weak transcription	Hela-S3	cervix
6	chr6:37872000-37887600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:37872000-37888200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:37872000-37890400	Weak transcription	Small Intestine	intestine
9	chr6:37872200-37884600	Weak transcription	Fetal Kidney	kidney
10	chr6:37872600-37885200	Weak transcription	HepG2	liver
11	chr6:37872600-37896400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:37873200-37887400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:37873400-37929200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:37874000-37888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:37874200-37884600	Weak transcription	A549	lung
16	chr6:37874400-37887600	Weak transcription	Spleen	Spleen
17	chr6:37874400-37888200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr6:37874600-37903800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:37876600-37903200	Weak transcription	Dnd41	blood
20	chr6:37878800-37900400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr6:37879600-37889600	Weak transcription	K562	blood
22	chr6:37879800-37886200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:37879800-37887400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:37879800-37887600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr6:37879800-37890400	Weak transcription	GM12878-XiMat	blood
26	chr6:37880000-37885000	Weak transcription	Stomach Mucosa	stomach
27	chr6:37880000-37887600	Weak transcription	Right Atrium	heart
28	chr6:37880000-37888400	Weak transcription	Gastric	stomach
29	chr6:37880000-37888600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:37880000-37889600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:37880000-37890800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr6:37880000-37892200	Weak transcription	Ovary	ovary
33	chr6:37880000-37896600	Weak transcription	Right Ventricle	heart
34	chr6:37880000-37898000	Weak transcription	Fetal Thymus	thymus
35	chr6:37880200-37887400	Weak transcription	Colon Smooth Muscle	Colon
36	chr6:37880200-37888200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:37880200-37930000	Weak transcription	Thymus	Thymus
38	chr6:37880400-37889200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr6:37880800-37885000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:37881200-37887600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:37881200-37890200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:37881400-37887400	Weak transcription	NH-A	brain
43	chr6:37881400-37887800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr6:37881400-37888200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr6:37881400-37895000	Weak transcription	Left Ventricle	heart
46	chr6:37881400-37896000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr6:37881600-37886200	Weak transcription	Fetal Stomach	stomach
48	chr6:37882000-37888200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:37882200-37888600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:37882200-37888600	Weak transcription	Fetal Muscle Leg	muscle

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